Admiral Nimitz had one significant advantage: American cryptanalysts had partially cracked the JN-25b code used by the Japanese Navy. The United States had been decoding information indicating that an action at objective "AF" would shortly take place since the beginning of 1942.

The location of "AF" was initially unknown, but Commander Joseph Rochefort and his team at Station HYPO were able to confirm that it was Midway: Captain Wilfred Holmes came up with a ruse to trick the base at Midway into broadcasting an uncoded radio message claiming that Midway's water purification system had malfunctioned (by means of a secure undersea communications cable).  The codebreakers discovered a Japanese communication stating that the "AF was short on water" within 24 hours.

Japan had a new codebook, but because of a delay in its implementation, HYPO was able to read messages for a number of vital days. The new code, which took some time to decipher, was finally put into use on May 24th, but the key cracks had already been made.

As a result, the Americans had a clear idea of where, when, and how strong the Japanese would show up at the battle. Nimitz was aware that the Japanese had divided his ships into four distinct task groups that were so far apart that they were essentially unable to reinforce one another, negating their numerical superiority. Few quick ships were available to escort the Carrier Striking Force as a result of this dispersion, which diminished the number of anti-aircraft guns defending the carriers.

Because American carrier air groups were larger than Japanese ones, Nimitz determined that the U.S. had roughly equal air power against Yamamoto's four carriers thanks to the aircraft on his three carriers and those on Midway Island. Contrarily, even after the conflict started, the Japanese were mostly ignorant of their enemy's true strength and dispositions.